Plate layout

Shows the layout of samples, controls (e.g., negative controls (NC), inter-plate controls (IPC)), and special wells if any (e.g., sample controls (SC), bridge samples) on the 96 well assay plate.

Plate 1: Plate Layout
1 2 3 4 5 6 7 8 9 10 11 12
A SMI A1 Donor01 SMI A2 Donor02 SMI A3 Donor03 SMI A4 Donor04 SMI A5 Donor05 SMI A6 Donor06 SMI A7 Donor07 SMI A8 Donor08 SMI A9 Donor09 SMI A10 Donor10 SMI A11 PP01 rep01 SMI A12 IPC rep01
B SMI B1 Donor11 SMI B2 Donor12 SMI B3 Donor13 SMI B4 Donor14 SMI B5 Donor15 SMI B6 Donor16 SMI B7 Donor17 SMI B8 Donor18 SMI B9 Donor19 SMI B10 Donor20 SMI B11 PP01 rep02 SMI B12 IPC rep02
C SMI C1 Donor21 SMI C2 Donor22 SMI C3 Donor23 SMI C4 Donor24 SMI C5 Donor25 SMI C6 Donor26 SMI C7 Donor27 SMI C8 Donor28 SMI C9 Donor29 SMI C10 Donor30 SMI C11 PP01 rep03 SMI C12 IPC rep03
D SMI D1 Donor31 SMI D2 Donor32 SMI D3 Donor33 SMI D4 Donor34 SMI D5 Donor35 SMI D6 Donor36 SMI D7 Donor37 SMI D8 Donor38 SMI D9 Donor39 SMI D10 Donor40 SMI D11 PP01 rep04 SMI D12 IPC rep04
E SMI E1 Donor41 SMI E2 Donor42 SMI E3 Donor43 SMI E4 Donor44 SMI E5 Donor45 SMI E6 Donor46 SMI E7 Donor47 SMI E8 Donor48 SMI E9 Donor49 SMI E10 Donor50 SMI E11 PP02 rep01 SMI E12 NTC rep01
F SMI F1 Donor51 SMI F2 Donor52 SMI F3 Donor53 SMI F4 Donor54 SMI F5 Donor55 SMI F6 Donor56 SMI F7 Donor57 SMI F8 Donor58 SMI F9 Donor59 SMI F10 Donor60 SMI F11 PP02 rep02 SMI F12 NTC rep02
G SMI G1 Donor61 SMI G2 Donor62 SMI G3 Donor63 SMI G4 Donor64 SMI G5 Donor65 SMI G6 Donor66 SMI G7 Donor67 SMI G8 Donor68 SMI G9 Donor69 SMI G10 Donor70 SMI G11 PP02 rep03 SMI G12 NTC rep03
H SMI H1 Donor71 SMI H2 Donor72 SMI H3 Donor73 SMI H4 Donor74 SMI H5 Donor75 SMI H6 Donor76 SMI H7 Donor77 SMI H8 Donor78 SMI H9 Donor79 SMI H10 Donor80 SMI H11 PP02 rep04 SMI H12 NTC rep04
Plate 2: Plate Layout
1 2 3 4 5 6 7 8 9 10 11 12
A SMI A1 Donor01 SMI A2 Donor02 SMI A3 Donor03 SMI A4 Donor04 SMI A5 Donor05 SMI A6 Donor06 SMI A7 Donor07 SMI A8 Donor08 SMI A9 Donor09 SMI A10 Donor10 SMI A11 PP01 rep01 SMI A12 IPC rep01
B SMI B1 Donor11 SMI B2 Donor12 SMI B3 Donor13 SMI B4 Donor14 SMI B5 Donor15 SMI B6 Donor16 SMI B7 Donor17 SMI B8 Donor18 SMI B9 Donor19 SMI B10 Donor20 SMI B11 PP01 rep02 SMI B12 IPC rep02
C SMI C1 Donor21 SMI C2 Donor22 SMI C3 Donor23 SMI C4 Donor24 SMI C5 Donor25 SMI C6 Donor26 SMI C7 Donor27 SMI C8 Donor28 SMI C9 Donor29 SMI C10 Donor30 SMI C11 PP01 rep03 SMI C12 IPC rep03
D SMI D1 Donor31 SMI D2 Donor32 SMI D3 Donor33 SMI D4 Donor34 SMI D5 Donor35 SMI D6 Donor36 SMI D7 Donor37 SMI D8 Donor38 SMI D9 Donor39 SMI D10 Donor40 SMI D11 PP01 rep04 SMI D12 IPC rep04
E SMI E1 Donor41 SMI E2 Donor42 SMI E3 Donor43 SMI E4 Donor44 SMI E5 Donor45 SMI E6 Donor46 SMI E7 Donor47 SMI E8 Donor48 SMI E9 Donor49 SMI E10 Donor50 SMI E11 PP02 rep01 SMI E12 NTC rep01
F SMI F1 Donor51 SMI F2 Donor52 SMI F3 Donor53 SMI F4 Donor54 SMI F5 Donor55 SMI F6 Donor56 SMI F7 Donor57 SMI F8 Donor58 SMI F9 Donor59 SMI F10 Donor60 SMI F11 PP02 rep02 SMI F12 NTC rep02
G SMI G1 Donor61 SMI G2 Donor62 SMI G3 Donor63 SMI G4 Donor64 SMI G5 Donor65 SMI G6 Donor66 SMI G7 Donor67 SMI G8 Donor68 SMI G9 Donor69 SMI G10 Donor70 SMI G11 PP02 rep03 SMI G12 NTC rep03
H SMI H1 Donor71 SMI H2 Donor72 SMI H3 Donor73 SMI H4 Donor74 SMI H5 Donor75 SMI H6 Donor76 SMI H7 Donor77 SMI H8 Donor78 SMI H9 Donor79 SMI H10 Donor80 SMI H11 PP02 rep04 SMI H12 NTC rep04

Read summary

Summary of the number and classification of reads for the assay run

Total reads Parseable Parseable Match Parseable Non-match Unparseable Total samples Total targets Total samples * targets Zero values
Plate 1 557,800,321 443,499,234 (79.5%) 320,863,871 (57.5%) 122,635,363 (22.0%) 114,301,087 (20.5%) 96 212 20,352 651 (3.2%)
Plate 2 551,437,639 444,325,042 (80.6%) 293,409,577 (53.2%) 150,915,465 (27.4%) 107,112,597 (19.4%) 96 212 20,352 622 (3.1%)

Internal controls (IC)

Each sample of the assay is spiked with the same concentration of an internal control (IC). This is used both as part of a well normalization procedure and as a method for assessing the uniformity of the assay run.

mCherry (IC) summary
Zeros n (%) Total reads (%) Mean SD CV%
Plate1 0 (0.0%) 575,548 (0.2%) 5,995.3 3,314.8 55.3%
Plate2 0 (0.0%) 783,521 (0.3%) 8,161.7 583.8 7.2%

Inter-plate controls (IPC)

IPC samples are pooled plasma controls used both to normalize samples between experiments and to assess performance (e.g., precision) of the assay.

Note: %CV in this table does not exclude values below LOD. See Intra-plate normalization or Inter-plate normalization sections for %CV (before and after normalization) that excludes values below LOD.

Plate 1: IPC summary
Total count (%) Mean count per target Zeros n (%) CV% mean CV% median
Total 4,216,763 (1.3%) 4,972.6 20 (2.4%) 12.9% 11.8%
SMI_A12_IPC_rep01 954,338 (0.3%) 4,501.6 5 (2.4%)
SMI_B12_IPC_rep02 983,653 (0.3%) 4,639.9 5 (2.4%)
SMI_C12_IPC_rep03 1,079,936 (0.3%) 5,094.0 5 (2.4%)
SMI_D12_IPC_rep04 1,198,836 (0.4%) 5,654.9 5 (2.4%)
Median 1,035,337 (0.3%) 4,883.7 5 (2.4%)
Plate 2: IPC summary
Total count (%) Mean count per target Zeros n (%) CV% mean CV% median
Total 5,595,993 (1.9%) 6,599.0 20 (2.4%) 9.9% 8.9%
SMI_A12_IPC_rep01 1,262,671 (0.4%) 5,956.0 5 (2.4%)
SMI_B12_IPC_rep02 1,382,933 (0.5%) 6,523.3 5 (2.4%)
SMI_C12_IPC_rep03 1,501,697 (0.5%) 7,083.5 5 (2.4%)
SMI_D12_IPC_rep04 1,448,692 (0.5%) 6,833.5 5 (2.4%)
Median 1,411,886 (0.5%) 6,659.8 5 (2.4%)

Negative controls (NC)

NC wells are reactions where no sample input is provided (i.e., buffer only). These are used to assess Limit of Detection (LOD) for each target assay and to assess run quality (e.g., background levels).

Plate 1: NC summary
Total count (%) Mean count per target Max target count Missing n (%)
NC total 252,207.00 (0.1%) 297.4 184 (21.7%)
SMI_E12_NTC_rep01 60,385.00 (0.0%) 284.8 23,356 47 (22.2%)
SMI_F12_NTC_rep02 64,471.00 (0.0%) 304.1 24,663 47 (22.2%)
SMI_G12_NTC_rep03 69,440.00 (0.0%) 327.5 26,829 42 (19.8%)
SMI_H12_NTC_rep04 57,911.00 (0.0%) 273.2 22,004 48 (22.6%)
NC means 63,051.75 (0.0%) 297.4 24,213.0 24 (11.3%)
Plate 2: NC summary
Total count (%) Mean count per target Max target count Missing n (%)
NC total 351,563.00 (0.1%) 414.6 160 (18.9%)
SMI_E12_NTC_rep01 90,306.00 (0.0%) 426.0 35,290 38 (17.9%)
SMI_F12_NTC_rep02 87,079.00 (0.0%) 410.8 33,650 43 (20.3%)
SMI_G12_NTC_rep03 89,527.00 (0.0%) 422.3 34,413 37 (17.5%)
SMI_H12_NTC_rep04 84,651.00 (0.0%) 399.3 32,520 42 (19.8%)
NC means 87,890.75 (0.0%) 414.6 33,968.2 14 ( 6.6%)

Sample controls (SC)

SC samples are pooled plasma controls from an independent pooled plasma source that is different from IPCs. They could be a pooled sample derived from all study samples, for example. They should be from the same source across all plates that will be analysed together. SCs are used for calculating intra- and inter-plate coefficient of variation (CV). They are necessary for obtaining an unbiased measure of inter-plate CV when IPC normalization is used.

Plate 1: SC summary
Total count (%) Mean count per target Zeros n (%) CV% mean CV% median
Total 9,478,631 (3.0%) 5,588.8 40 (2.4%) 17.4% 12.1%
SMI_A11_PP01_rep01 875,429 (0.3%) 4,129.4 5 (2.4%)
SMI_B11_PP01_rep02 798,857 (0.2%) 3,768.2 5 (2.4%)
SMI_C11_PP01_rep03 879,134 (0.3%) 4,146.9 5 (2.4%)
SMI_D11_PP01_rep04 924,573 (0.3%) 4,361.2 5 (2.4%)
SMI_E11_PP02_rep01 1,482,992 (0.5%) 6,995.2 5 (2.4%)
SMI_F11_PP02_rep02 1,663,813 (0.5%) 7,848.2 5 (2.4%)
SMI_G11_PP02_rep03 1,465,841 (0.5%) 6,914.3 5 (2.4%)
SMI_H11_PP02_rep04 1,387,992 (0.4%) 6,547.1 5 (2.4%)
Median 1,156,082 (0.4%) 5,453.2 5 (2.4%)
Plate 2: SC summary
Total count (%) Mean count per target Zeros n (%) CV% mean CV% median
Total 14,890,863 (5.1%) 8,780.0 40 (2.4%) 17.6% 12.6%
SMI_A11_PP01_rep01 1,218,397 (0.4%) 5,747.2 5 (2.4%)
SMI_B11_PP01_rep02 1,257,936 (0.4%) 5,933.7 5 (2.4%)
SMI_C11_PP01_rep03 1,346,170 (0.5%) 6,349.9 5 (2.4%)
SMI_D11_PP01_rep04 1,332,188 (0.5%) 6,283.9 5 (2.4%)
SMI_E11_PP02_rep01 2,314,772 (0.8%) 10,918.7 5 (2.4%)
SMI_F11_PP02_rep02 2,584,480 (0.9%) 12,190.9 5 (2.4%)
SMI_G11_PP02_rep03 2,474,138 (0.8%) 11,670.5 5 (2.4%)
SMI_H11_PP02_rep04 2,362,782 (0.8%) 11,145.2 5 (2.4%)
Median 1,827,886 (0.6%) 8,622.1 5 (2.4%)

Heatmaps

Heatmaps show the percent relative to plate median for log2(total counts) and the specified internal control.

Quality control

Plate QC

Plate-specific QC criteria:

  • ICRead_CV - Coefficient of Variation of internal control signal across all samples (maximum = 50%)
  • IPCRead_CV - Coefficient of Variation of the total assay signal across all IPCs (maximum = 50%)
  • IPCTarget_CV - Median Coefficient of Variation of all IPC targets (maximum = 20%)
  • Detectability - Percentage of targets that are detectable (target is considered detectable if > 50% samples have signal > LOD) (minimum = 75%)
  • MinReads - Number of total Parseable Match reads (signal) for the experiment (minimum = 5e+05)

QC criteria are assessed either on unnormalized (raw) or IC-normalized (IC) data.

Plate 1: Plate QC Summary
QC Criterion Normalization QC Status QC Value QC Threshold
ICRead_CV raw Warning 55.3% 50%
IPCRead_CV raw Pass 10.5% 50%
IPCTarget_CV IC Pass 8.2% 20%
Detectability IC Pass 91.9% 75%
MinReads raw Pass 320,863,871 5e+05
Plate 2: Plate QC Summary
QC Criterion Normalization QC Status QC Value QC Threshold
ICRead_CV raw Pass 7.2% 50%
IPCRead_CV raw Pass 7.4% 50%
IPCTarget_CV IC Pass 5.5% 20%
Detectability IC Pass 91.9% 75%
MinReads raw Pass 293,409,577 5e+05

Sample QC

Sample QC summary tables

Sample-specific QC criteria:

  • Detectability - Percentage of targets above LOD for a sample (minimum = 80%)
  • ICReads - Number of IC reads for a sample (minimum = 1000)
  • NumReads - Number of total Parseable Match (signal) reads for a sample (minimum = 5e+05)
  • IC_Median - % deviation from the overall plate median IC reads (within +/-30% of plate median)
Number of samples that fail each QC criterion (excludes IPC, SC, NC & bridge samples)
# of Samples Detectability ICReads NumReads IC_Median
Plate 1 80 1 0 0 1
Plate 2 80 0 0 0 0
Total 160 1 0 0 1
Samples that fail Detectability
Plate QC_fail_samples
Plate 1 SMI_G5_Donor65
Samples that fail IC_Median
Plate QC_fail_samples
Plate 1 SMI_G5_Donor65

Sample QC plots

Detectability

Target detectability is the percentage of samples that are above the limit of detection for that target. A target is considered “detectable” if it is above limit of detection in greater than 50% of samples. “Overall” detectability is the overall percentage of samples across all plates that are above LOD for a given target. Target detectability reported here excludes IPCs, SCs, NCs, and bridge samples.

Detectability summary

type # samples mean sd median min max # of detectable targets (%)
Plate 1 all 80 91.1 24.2 100 0 100 194 (91.9%)
Plate 2 all 80 91.0 24.1 100 0 100 194 (91.9%)
Overall all 160 91.0 23.9 100 0 100 194 (91.9%)

Target detectability %

Plate 1 Plate 2 Overall
Activin AB 65.0 37.5 51.25
AGER 100.0 100.0 100
AGRP 100.0 100.0 100
ANGPT1 100.0 100.0 100
ANXA1 76.2 81.2 78.7
BDNF 100.0 100.0 100
BMP10 72.5 73.8 73.15
BMP15 0.0 0.0 0
BMP7 100.0 100.0 100
C1QA 100.0 100.0 100
CCL1 100.0 100.0 100
CCL13 100.0 100.0 100
CCL14 100.0 100.0 100
CCL15 100.0 100.0 100
CCL16 100.0 100.0 100
CCL17 100.0 100.0 100
CCL19 100.0 100.0 100
CCL2 100.0 100.0 100
CCL20 100.0 100.0 100
CCL22 100.0 100.0 100
CCL23 100.0 100.0 100
CCL24 100.0 100.0 100
CCL25 100.0 100.0 100
CCL28 100.0 100.0 100
CCL3 22.5 48.8 35.65
CCL4 100.0 100.0 100
CCL5 100.0 100.0 100
CCL7 98.8 100.0 99.4
CCL8 100.0 100.0 100
CD200 92.5 95.0 93.75
CD200R1 100.0 100.0 100
CD274 100.0 100.0 100
CD276 100.0 100.0 100
CD40 100.0 100.0 100
CD70 83.8 56.2 70
CD83 100.0 100.0 100
CD93 100.0 100.0 100
CEACAM5 100.0 100.0 100
CHI3L1 100.0 100.0 100
CLCF1 13.8 53.8 33.8
CLEC4A 100.0 100.0 100
CSF1 100.0 100.0 100
CSF2 0.0 1.2 0.6
CSF2RB 85.0 87.5 86.25
CSF3 100.0 100.0 100
CSF3R 100.0 100.0 100
CST7 100.0 100.0 100
CTF1 100.0 100.0 100
CTLA4 100.0 100.0 100
CTSS 100.0 100.0 100
CX3CL1 100.0 100.0 100
CXADR 100.0 100.0 100
CXCL1 100.0 100.0 100
CXCL10 100.0 100.0 100
CXCL12 100.0 100.0 100
CXCL13 100.0 100.0 100
CXCL14 98.8 100.0 99.4
CXCL2 100.0 100.0 100
CXCL3 100.0 100.0 100
CXCL5 100.0 100.0 100
CXCL8 100.0 100.0 100
CXCL9 100.0 100.0 100
EBI3 37.5 42.5 40
EGF 100.0 100.0 100
EPO 100.0 100.0 100
FAM3C 0.0 0.0 0
FAM3D 100.0 100.0 100
FASLG 100.0 100.0 100
FGF19 100.0 100.0 100
FGF2 93.8 98.8 96.3
FGF21 100.0 100.0 100
FGF23 100.0 100.0 100
FGF5 0.0 0.0 0
FLT1 100.0 100.0 100
FLT3LG 20.0 11.2 15.6
FTH1 100.0 100.0 100
GDF15 100.0 100.0 100
GDF2 100.0 100.0 100
GFAP 100.0 100.0 100
GRN 100.0 100.0 100
GZMB 100.0 100.0 100
HGF 100.0 100.0 100
IFNA1; IFNA13 98.8 100.0 99.4
IFNA2 52.5 60.0 56.25
IFNB1 95.0 100.0 97.5
IFNG 100.0 100.0 100
IFNL1 100.0 100.0 100
IFNW1 41.2 28.7 34.95
IL10 100.0 100.0 100
IL10RB 100.0 100.0 100
IL11 100.0 93.8 96.9
IL12B 100.0 100.0 100
IL12p70 95.0 98.8 96.9
IL12RB1 100.0 100.0 100
IL13 100.0 100.0 100
IL13RA2 100.0 100.0 100
IL15RA 100.0 100.0 100
IL16 100.0 100.0 100
IL17A 98.8 100.0 99.4
IL17B 100.0 100.0 100
IL17C 100.0 100.0 100
IL17F 98.8 100.0 99.4
IL17RB 100.0 100.0 100
IL18 100.0 100.0 100
IL18BP 100.0 100.0 100
IL18R1 100.0 100.0 100
IL19 98.8 100.0 99.4
IL1B 58.8 47.5 53.15
IL1R1 0.0 0.0 0
IL1R2 100.0 100.0 100
IL1RL1 100.0 100.0 100
IL1RN 98.8 100.0 99.4
IL20 100.0 100.0 100
IL22 61.3 71.2 66.25
IL23 98.8 98.8 98.8
IL2RA 100.0 100.0 100
IL2RB 100.0 100.0 100
IL32 91.2 58.8 75
IL33 98.8 100.0 99.4
IL34 100.0 98.8 99.4
IL35 2.5 3.8 3.15
IL36A 100.0 100.0 100
IL36G 91.2 77.5 84.35
IL39 6.2 7.5 6.85
IL3RA 100.0 100.0 100
IL4 100.0 100.0 100
IL4R 100.0 100.0 100
IL5 100.0 100.0 100
IL5RA 100.0 100.0 100
IL6 98.8 97.5 98.15
IL6R 100.0 100.0 100
IL7 100.0 100.0 100
IL7R 100.0 100.0 100
IL9 100.0 100.0 100
INHBA 87.5 71.2 79.35
INHBB 80.0 56.2 68.1
Inhibin A 25.0 13.8 19.4
Inhibin B 35.0 65.0 50
IRAK4 100.0 98.8 99.4
KDR 100.0 100.0 100
KITLG 98.8 100.0 99.4
LAG3 100.0 100.0 100
LAMP3 98.8 100.0 99.4
LCN2 100.0 100.0 100
LGALS9 95.0 100.0 97.5
LIF 98.8 100.0 99.4
LTBR 100.0 100.0 100
MDK 100.0 100.0 100
MERTK 100.0 100.0 100
MET 100.0 100.0 100
MICA 85.0 90.0 87.5
MICB 100.0 100.0 100
MIF 100.0 100.0 100
MMP10 100.0 100.0 100
MMP12 98.8 100.0 99.4
MMP3 100.0 100.0 100
MMP8 100.0 100.0 100
MMP9 100.0 100.0 100
MPO 100.0 100.0 100
MUC16 100.0 100.0 100
NCR1 100.0 100.0 100
NGF 100.0 100.0 100
NIC_1 0.0 7.5 3.75
NIC_3 0.0 0.0 0
OSM 100.0 100.0 100
PDCD1 100.0 100.0 100
PDGFA 100.0 100.0 100
PTX3 100.0 100.0 100
S100A12 100.0 100.0 100
S100A9 88.8 92.5 90.65
SCG2 98.8 100.0 99.4
SELE 100.0 100.0 100
SLURP1 100.0 100.0 100
SPP1 100.0 100.0 100
TAFA5 100.0 100.0 100
TGFB1 100.0 100.0 100
TGFB3 80.0 97.5 88.75
THPO 100.0 100.0 100
TIMP1 100.0 100.0 100
TIMP2 100.0 100.0 100
TLR3 100.0 100.0 100
TNF 86.2 77.5 81.85
TNFRSF11A 100.0 100.0 100
TNFRSF13C 100.0 100.0 100
TNFRSF14 100.0 100.0 100
TNFRSF17 100.0 100.0 100
TNFRSF18 100.0 97.5 98.75
TNFRSF1A 100.0 100.0 100
TNFRSF1B 100.0 100.0 100
TNFRSF4 100.0 100.0 100
TNFRSF8 100.0 100.0 100
TNFRSF9 100.0 100.0 100
TNFSF10 100.0 100.0 100
TNFSF11 92.5 62.5 77.5
TNFSF12 100.0 100.0 100
TNFSF13 100.0 100.0 100
TNFSF13B 98.8 100.0 99.4
TNFSF15 100.0 100.0 100
TNFSF4 100.0 100.0 100
TNFSF8 100.0 100.0 100
TNFSF9 100.0 100.0 100
TREM1 100.0 100.0 100
TSLP 100.0 100.0 100
VCAM1 100.0 100.0 100
VEGFA 37.5 36.2 36.85
VEGFC 100.0 100.0 100
VEGFD 88.8 96.2 92.5
VSNL1 100.0 100.0 100
VSTM1 97.5 100.0 98.75
WNT16 100.0 100.0 100
WNT7A 100.0 100.0 100

Target detectability boxplot

Plot shows target mCherry-IPC-normalized count distributions relative to LOD. For each target, log2(LOD) was subtracted from log2(count) for mCherry-normalized data.

Intra-plate normalization

%CV was calculated for each target (excluding internal controls) for the sample control replicates (if given) and IPCs. Only values above LOD were used to calculate %CV. If there are multiple plates, “Overall” represents the distribution for the target-specific mean intra-plate CV across all plates.

Intra-plate normalization

%CV was calculated for each target (excluding internal controls) for the sample control replicates (if given) and IPCs. Only values above LOD were used to calculate %CV.

Intra-plate %CV table – unnormalized

SC intra-plate %CV – unnormalized
mean sd median min max missing
Plate 1 15.6 13.8 11.2 2.050 106 10
Plate 2 16.1 14.5 12.4 0.452 105 12
Overall 15.8 13.8 11.6 2.050 105 10
IPC intra-plate %CV – unnormalized
mean sd median min max missing
Plate 1 11.99 3.67 11.66 1.48 30.0 14
Plate 2 9.33 3.73 8.77 2.38 27.2 16
Overall 10.68 2.80 10.32 3.84 21.6 14

Intra-plate %CV table – mCherry-normalized

SC intra-plate %CV – mCherry-normalized
mean sd median min max missing
Plate 1 15.1 13.7 11.2 1.23 105 10
Plate 2 14.8 14.7 11.2 1.74 105 12
Overall 14.9 13.8 10.9 1.23 105 10
IPC intra-plate %CV – mCherry-normalized
mean sd median min max missing
Plate 1 8.77 3.81 8.08 1.89 26.8 14
Plate 2 6.38 3.87 5.48 1.40 23.7 16
Overall 7.61 3.23 6.72 3.46 24.3 14

Intra-plate %CV boxplots by plate

Sample boxplots

Sample boxplots show distributions of the log2 counts for each sample, unnormalized and after mCherry + IPC normalization.

Sample correlation

Plot shows the Pearson correlation between samples. Heirarchical clustering is done using complete linkage.

Sample and target clustering

Hierarchical clustering of both samples and targets was done using a Euclidean distance metric and complete linkage. Data is log2 and mCherry-normalized; targets are centered and scaled.

Inter-plate normalization

%CV was calculated for each target (excluding internal controls) for the sample control replicates. Only values above LOD were used to calculate %CV.

Inter-plate %CV

SC inter-plate %CV
mean sd median min max missing
unnorm 28.0 11.6 25.5 2.05 108 10
mCherry 16.7 13.0 13.3 1.23 103 10
mCherry + IPC 17.3 13.0 13.9 1.23 103 10
mCherry + IN 17.8 13.0 14.6 1.23 102 10
IPC inter-plate %CV
mean sd median min max missing
unnorm 17.72 3.27 17.64 5.73 28.0 13
mCherry 8.10 3.49 7.17 3.90 22.6 13
mCherry + IPC 7.44 3.21 6.68 1.79 22.9 13
mCherry + IN 9.23 4.23 7.87 3.73 28.4 13

Inter-plate %CV boxplot

Sample PCA